Journal of Computational Chemistry

Cover image for Vol. 34 Issue 14

30 May 2013

Volume 34, Issue 14

Pages i–iv, 1177–1269

  1. Cover Image

    1. Top of page
    2. Cover Image
    3. Feature Articles
    4. Full Papers
    1. You have free access to this content
      Cover Image, Volume 34, Issue 14 (pages i–ii)

      Version of Record online: 20 APR 2013 | DOI: 10.1002/jcc.23313

      Thumbnail image of graphical abstract

      Molecular footprints, which encode interaction energy patterns (maps) between a ligand and its target, can be useful for rational drug design as reported by Trent Balius, William Allen, Sudipto Mukherjee, and Robert Rizzo on page 1226. Strong overlap between footprints indicates similar interaction signatures and can be used to prioritize compounds from virtual screening or guide de novo design. The cover shows a small molecule constructed to mimic the footprint pattern made by four key sidechains on the native substrate, which binds the viral fusion protein HIVgp41.

    2. You have free access to this content
      Inside Cover, Volume 34, Issue 14 (pages iii–iv)

      Version of Record online: 20 APR 2013 | DOI: 10.1002/jcc.23314

      Thumbnail image of graphical abstract

      A coarse-grain model is used by Sandra Nunes et al. on page 1198 to study the conformation and adsorption patterns of polyelectrolytes of various lengths onto oppositely charged surfaces that have different areas and charge densities. High surface charge densities always impose some degree of compaction, irrespective of the available space. Surfaces of a lower charge density can adsorb more chain segments for the same, small number of surface charges. The potential field created in these regularly charged surfaces is nonuniform, promoting a preferential occupancy of some regions. These are selected by a balance between the maximization of the polyelectrolyte/surface electrostatic interaction and the minimization of the backbone bending penalty.

  2. Feature Articles

    1. Top of page
    2. Cover Image
    3. Feature Articles
    4. Full Papers
    1. Grand challenges in quantum-classical modeling of molecule–surface interactions (pages 1177–1188)

      Claudia R. Herbers, Chunli Li and Nico F. A. van der Vegt

      Version of Record online: 19 FEB 2013 | DOI: 10.1002/jcc.23247

      Thumbnail image of graphical abstract

      The state of the art of the force field development of molecule-surface interactions is reviewed. The image shows an ethanol molecule adsorbing on an alumina surface.

    2. Exact ligand cone angles (pages 1189–1197)

      Jenna A. Bilbrey, Arianna H. Kazez, Jason Locklin and Wesley D. Allen

      Version of Record online: 13 FEB 2013 | DOI: 10.1002/jcc.23217

      Thumbnail image of graphical abstract

      A mathematically rigorous method is derived for determining exact ligand cone angles and is applied to over 150 complexes of phosphine and amine ligands bound to palladium, nickel, or platinum, as optimized by B3LYP/6-31G* density functional theory with effective core potentials.

  3. Full Papers

    1. Top of page
    2. Cover Image
    3. Feature Articles
    4. Full Papers
    1. Nonrandom adsorption of polyelectrolyte chains on finite regularly charged surfaces (pages 1198–1209)

      Sandra C. C. Nunes, P. Pinto and A. A. C. C. Pais

      Version of Record online: 5 FEB 2013 | DOI: 10.1002/jcc.23238

      Thumbnail image of graphical abstract

      Finite surfaces characterized by a regular distribution of charges create a nonuniform potential. Oppositely charged polyelectrolyte backbones tend to adsorb in regions of the surface that maximize the electrostatic interaction, while ensuring the minimal bending penalty. This results in characteristic nonuniform adsorption patterns.

    2. The adaptive hierarchical expansion of the kinetic energy operator (pages 1210–1217)

      Daniel Strobusch, Mathias Nest and Christoph Scheurer

      Version of Record online: 8 APR 2013 | DOI: 10.1002/jcc.23241

      Thumbnail image of graphical abstract

      A new analytical estimate allows for the adaptive simplification of the recently introduced hierarchical expansion of the kinetic energy operator, thus greatly reducing its computational complexity.

    3. Linearity condition for orbital energies in density functional theory (III): Benchmark of total energies (pages 1218–1225)

      Yutaka Imamura, Rie Kobayashi and Hiromi Nakai

      Version of Record online: 13 FEB 2013 | DOI: 10.1002/jcc.23243

      Thumbnail image of graphical abstract

      The orbital-specific (OS) hybrid functionals, designed to satisfy the linearity condition for orbital energies (LCOE), can provide accurate total energies. Numerical assessment shows that total energies for He, He+, and He2+ are well reproduced by the OS hybrid functional in comparison with the conventional one. The assessment guarantees that the LCOE offers an accurate description of orbital energies and total energies.

    4. Grid-based molecular footprint comparison method for docking and de novo design: Application to HIVgp41 (pages 1226–1240)

      Trent E. Balius, William J. Allen, Sudipto Mukherjee and Robert C. Rizzo

      Version of Record online: 22 FEB 2013 | DOI: 10.1002/jcc.23245

      Thumbnail image of graphical abstract

      A new multigrid implementation of the molecular footprint similarity (FPS) scoring function is developed, wherein lead discovery or design can be targeted specifically to match important conserved protein-ligand interactions. This provides improved pose reproduction, crossdocking, and enrichment over the standard DOCK function. De novo design tests suggest that the method can be used to tailor the construction of new molecules to have specific properties in a computationally tractable time.

    5. Polarizable simulations with second order interaction model (POSSIM) force field: Developing parameters for protein side-chain analogues (pages 1241–1250)

      Xinbi Li, Sergei Y. Ponomarev, Qina Sa, Daniel L. Sigalovsky and George A. Kaminski

      Version of Record online: 19 FEB 2013 | DOI: 10.1002/jcc.23248

      Thumbnail image of graphical abstract

      A fast polarizable formalism, Polarizable Simulations with Second Order Interaction Model (POSSIM) software, and force field parameters for several systems were previously introcuced. Extension of the set of parameters to include analogues of protein side chains are now reported. These results can be used to simulate small organic molecules and their interactions in solutions. Hopefully this will lead to a broadening of the scope of applications of the POSSIM code and force field.

    6. Protein-specific force field derived from the fragment molecular orbital method can improve protein–ligand binding interactions (pages 1251–1257)

      Le Chang, Takeshi Ishikawa, Kazuo Kuwata and Shoji Takada

      Version of Record online: 19 FEB 2013 | DOI: 10.1002/jcc.23250

      Thumbnail image of graphical abstract

      Protein-specific partial charge distribution on the protein surface can improve the ability of in silico protein-ligand binding free energy calculations. The fragment molecular orbital method makes it possible to calculate the quantum mechanical electrostatic potential around the protein surface. Such electrostatic potential is used in the restrained electrostatic potential method to fit the partial charges on atoms in proteins.

    7. Systematic and efficient side chain optimization for molecular docking using a cheapest-path procedure (pages 1258–1269)

      Marcel Schumann and Roger S. Armen

      Version of Record online: 19 FEB 2013 | DOI: 10.1002/jcc.23251

      Thumbnail image of graphical abstract

      Modeling receptor side chain flexibility is important for molecular docking, as it allows the receptor to adopt new conformations as induced by ligand binding. A new docking approach with a very fast, graph-based optimization algorithm for assignment of the near-optimal set of residue rotamers is described. The approach is validated using the 40 DUD target benchmarks, and large improvement is demonstrated using the developed side chain optimization over rigid receptor docking.